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Pablo Baez Benavides, PhD
Education
Postdoctoral Researcher
University of Chile
Santiago, Chile
Present - Apr. 2021
- Fondecyt postdoctoral research grant: Linguistic characterization of the Chilean clinical text: towards an automatic extraction of information
Ph.D. in Biomedical Sciences
University of Chile
Santiago, Chile
Jan. 2018 - Mar. 2013
- Thesis: Genetic linkage and association analysis to identify genetic risk markers of cholelithiasis and gallbladder cancer in Chile.
M.S. in Biological Sciences, mention in Genetics
University of Chile
Santiago, Chile
Jun. 2013 - Apr. 2011
- Thesis: Role of the TRPM4 channel in the development of prostate cancer in a transgenic murine model.
B.S. Microbiology and Bioanalysis
University of Antioquia
Medellín, Colombia
May. 2009 - Jan. 2003
Research Experience
Researcher
Center for Mathematical Modeling, University of Chile
Santiago, Chile
Jul. 2021 - Jan. 2021
- Named entity recognition of tumor morphology and topography from surgical pathology reports.
- PI: Jocelyn Dunstan
Researcher
Center for Medical Informatics and Telemedicine, University of Chile
Santiago, Chile
Mar. 2021 - Jan. 2020
- Automatic analysis of clinical narratives produced in Chile using neural networks.
- PI: Jocelyn Dunstan
Researcher
Center for Medical Informatics and Telemedicine, University of Chile
Santiago, Chile
Dec. 2020 - Dec. 2019
- FONDEF IDeA I+D 2019 (2019-2021): “Deep-Pathology: Distributed TelePathology Platform Based on Blockchain and Collaborative Diagnosis Supported by Deep Learning”.
- PI: Steffen Härtel Gründler
Postdoctoral Researcher
Center for Medical Informatics and Telemedicine, University of Chile
Santiago, Chile
Dec 2019 - Sep. 2018
- Systematic analysis of family history in free text of electronic medical records.
PhD Candidate
Foundation for Advanced Biomedical Studies (FEBA), Faculty of Medicine, University of Chile
Santiago, Chile
Apr. 2018 - Dec. 2017
- Analysis of germline and somatic genetic variants in patients with gallbladder cancer.
PhD Student - Candidate
Cancer Genomics Laboratory, Faculty of Medicine, University of Chile
Santiago, Chile
Jan. 2018 - Aug. 2014
- Statistical analysis of socio-demographic information
- Genetic linkage analysis in families with multiple gallbladder cancer patients
- Fine mapping and genome wide association analysis in a case-control study
Graduate Student Fellow
Institute of Medical Biometry and Informatics (IMBI), University Hospital Heidelberg
Heidelberg, Germany
Feb. 2016 - Aug. 2015
- Trained in specialized bioinformatics tools (R, PLINK and Mendel) to analyze genetic data
- Attended the EMBL Conference: Cancer Genomics
- Attended scientific talks organized by the University of Heidelberg and the German Center for Oncological Research (dkfz)
Master’s student
Laboratory of Molecular Cancer Pathology, Faculty of Medicine, University of Chile
Santiago, Chile
Jun. 2013 - Mar. 2012
- Histopathological analysis of prostate, lymph nodes and lung sections of a murine model of prostate cancer (TRAMP mice)
- Quantification of mRNA using real-time RT-PCR on TRAMP mice prostates
Service
Diagnosis Foundation
Advisory member of the Diagnosis Foundation
Santiago, Chile
Dec. 2021 - Nov. 2019
- Support the diagnosis and research of unknown diseases
- Promote the knowledge generation through ethical and collaborative scientific research
Teaching Experience
I really enjoy teaching and sharing my experiences in health data science.
Undergraduate Teaching - Coordinating Professor
School of Medical Technology, Universidad del Desarrollo
Santiago, Chile
Present - Sep. 2023
- CB. Medical Informatics
- Course of the formative area of the Clinical Bioanalysis, Hematology and Blood Bank specialty, with 68 academic hours taught in the eighth semester of the Study Plan.
Undergraduate Methodological Advisor
School of Medical Technology, Universidad del Desarrollo
Santiago, Chile
Present - Sep. 2023
- Research Seminar
Graduate Teaching - Coordinating Professor
International Master in Medical Informatics, University of Chile
Santiago, Chile
Present - Aug. 2020
- CA. Bioinformatics I and II
Undergraduate Teaching - Coordinating Professor
School of Medical Technology, Universidad del Desarrollo
Santiago, Chile
Present - Aug. 2021
- CB. Bioinformatics in Molecular Diagnostics
- Course of the formative area of the Morphophysiopathology and Cytodiagnosis specialty, with 102 academic hours taught in the eighth semester of the Study Plan
Master Thesis Supervisor
International Master in Medical Informatics, University of Chile
Santiago, Chile
Jun. 2022 - Jul. 2021
- Automatic Staging of Distant Metastases in Imaging Reports Using Natural Language Processing
- Ricardo Ahumada’s Master Thesis Supervisor together with Jocelyn Dunstan PhD
Master Thesis Examiner
International Master in Medical Informatics, University of Chile
Santiago, Chile
Apr. 2022 - Jul. 2021
- Automatic transcription and extraction of key information from Spanish-language clinical audios
- Maicol Fernandez’s Master Thesis Examiner
Graduate Teaching - Guest Professor
International Master in Medical Informatics, University of Chile
Santiago, Chile
Jun. 2021
- CA. Statistical Analysis Methods II
- Language Resources Creation for NLP
Graduate Teaching - Guest Professor
International Master in Medical Informatics, University of Chile
Santiago, Chile
Jul. 2020 - May. 2020
- CB. Biostatistics I and II
Undergraduate Student Supervisor
Faculty of Medicine, University of Chile
Santiago, Chile
Dec. 2020 - Mar. 2020
- Research Unit I and II
- 40 hour tutoring of second-year medical students
- Guidance on the construction and execution of a short research project
Graduate Teaching - Guest Professor
International Master in Medical Informatics, University of Chile
Santiago, Chile
Oct. 2018
- CA. Biomedicine II
- Genetic epidemiology studies in cancer
Undergraduate Teaching - Guest Professor
School of Medical Technology, Universidad del Desarrollo
Santiago, Chile
Oct. 2018 - Aug. 2018
- CB. Scientific Bases of Medical Technology
Undergraduate Teaching - Guest Professor
School of Medical Technology, Universidad Mayor
Santiago, Chile
Sep. 2017
- CB. Applied Biotechnology
Undergraduate Student Supervisor
Faculty of Medicine, University of Chile
Santiago, Chile
Jan. 2017 - Mar. 2016
- Research Unit I and II
- 40 hour tutoring of second-year medical students
- Guidance on the construction and execution of a short research project
Undergraduate Teaching - Auxiliary Guest Professor
School of Medical Technology, ICBM, University of Chile
Santiago, Chile
May. 2015
- Seminars on the application of Molecular Biology
Publications
Soon you will also find some notes about my work, talks and side projects in my blog.
E-Learning Module for Cytopathology Education Based on Virtual Microscopy
Journal of the American Society of Cytopathology
Santiago, Chile
2023
- Cubillos, L., Diaz, E., Báez, P., Gutiérrez, L., Molina C., Härtel, S.
- (in press)
Amerindian Ancestry Proportion as a Risk Factor for Inflammatory Bowel Diseases: Results from a Latin American Andean Cohort
Frontiers in Medicine
Santiago, Chile
2023
- Pérez-Jeldres, T., Magne, F., Ascui, G., Alvares D., Orellana, M., Álvarez-Lobos, M., Hernández-Rocha, C., Azócar, L., Aguilar, N., Espino, A., Estela, R., Escobar, S., Zazueta, A., Baez, P., Silva, V., De La Vega, A., Arriagada, E., Pavez-Ovalle, C., Diaz-Asencio, A., Travisany, D., … Bustamante, M.L.
- (in press)
Genotype Prevalence of Lactose Deficiency, Vitamin D Deficiency, and the Vitamin D Receptor in a Chilean Inflammatory Bowel Disease Cohort: Insights from an Observational Study
International Journal of Molecular Sciences
Santiago, Chile
2023
Genome sequencing reveals molecular subgroups in oral epithelial dysplasia
Brazilian Oral Research
Santiago, Chile
2023
Natural language processing for clinical text in Spanish: The case of waiting lists in Chile
Revista Médica Clínica Las Condes, 2022, vol. 33, no 6, p. 576-582.
Santiago, Chile
2022
Ethnicity influences phenotype and clinical outcomes: Comparing a South American with a North American inflammatory bowel disease cohort
Medicine, September 09, 2022 - Volume 101 - Issue 36 - p e30216
Santiago, Chile
2022
Cáncer de vesícula en colecistectomías de la región de Tarapacá. Análisis según pertenencia étnica
Revista Médica de Chile, 150(9).
Santiago, Chile
2022
Automatic support system for tumor coding in pathology reports in Spanish
Preprint available at SSRN 3982259
Santiago, Chile
2022
Automatic Extraction of Nested Entities in Clinical Referrals in Spanish
ACM Transactions on Computing for Healthcare (HEALTH), 2022, vol. 3, no 3, p. 1-22.
Santiago, Chile
2022
Construcción de recursos de texto para la identificación automática de información clínica en narrativas no estructuradas
Revista Médica de Chile, 149(7).
Santiago, Chile
2021
Prevalencia de colecistolitiasis y cáncer de vesícula en una población rural Aymara de Chile
Revista Médica de Chile, 148(10).
Santiago, Chile
2020
The Chilean Waiting List Corpus: a new resource for Clinical Named Entity Recognition
Proceedings of the 3rd Clinical Natural Language Processing Workshop (pp. 291-300)
Santiago, Chile
2020
ABCB1/4 Gallbladder Cancer Risk Variants Identified in India Also Show Strong Effects in Chileans
Cancer Epidemiol. 2020 Apr;65:101643.
Santiago, Chile
2020
TRPM4 regulates Akt/GSK3-β activity and enhances β-catenin signaling and cell proliferation in prostate cancer cells
Mol Oncol. 2018 Feb; 12(2):151-165.
Santiago, Chile
2018
Subtypes of Native American ancestry and leading causes of death: Mapuche ancestry-specific associations with gallbladder cancer risk in Chile
PLoS Genet 13(5): e1006756.
Santiago, Chile
2017
Mast Cell Infiltration and Kit and Protease Expression During Progression of a Transgenic Prostate Cancer Murine Model (TRAMP)
Journal of Comparative Pathology, 150(1), 88.
Santiago, Chile
2014
- González, C., Armisén, R., Stutzin, A., Baez, P., Landerer, E., Paredes, R., Contreras, I., Muñoz, C.
Actualización en cáncer de próstata: generalidades y diagnóstico
Medicina & Laboratorio, 18, 7-8.
Santiago, Chile
2012
- Báez, P., Armisén Yañez, R.
Colonización por Staphylococcus aureus resistente a meticilina en las manos de individuos de la comunidad
Iatreia, 23(1), 5-9.
Medellín, Colombia
2010
- Báez, P., Zapata Tamayo, M., Ramírez Pérez, A., Rúa Giraldo, A., & Jiménez Quiceno, J.
Scholarships & Awards
Fondecyt Postdoctoral Research Grant
National Agency for Research and Development - ANID
Santiago, Chile
Apr. 2021
Best Paper
3rd Clinical Natural Language Processing Workshop. Paper title: The Chilean Waiting List Corpus: a new resource for Clinical Named Entity Recognition.
Clinical NLP Workshop, EMNLP
Nov. 19 2020
Postdoctoral Bridge Scholarship
Biomedical Neuroscience Institute (BNI), University of Chile
Santiago, Chile
Sep. 2018
Scholarship for Internship Abroad
MECESUP Program Uch1304, University of Chile
Santiago, Chile
Jul. 2015
CONICYT National PhD Scholarship for Foreigners
Ministry of Education, Government of Chile
Santiago, Chile
Mar. 2013
Master’s approval with maximum distinction
Postgraduate School, University of Chile
Santiago, Chile
Jun. 2013
Ten best results at national level according to academic program: ECAES test
Ministry of Education, Republic of Colombia
Medellín, Colombia
2008